These instructions assume you've got a Linux rig up and mining. If you followed the Installing Debian and Nvidia Mining guides you will be all set for this. Plug your Gridseed into the power supply and a USB port. If you use a USB hub make certain it's a powered hub.
Download and compile the modified CGMiner:
# cd /root
# git clone https://github.com/dtbartle/cgminer-gc3355
# cd cgminer-gc3355
# ./configure --enable-scrypt --enable-gridseed
# make
# git clone https://github.com/dtbartle/cgminer-gc3355
# cd cgminer-gc3355
# ./configure --enable-scrypt --enable-gridseed
# make
Run it:
# ./cgminer -o stratum+tcp://us.clevermining.com:3333 -u 1EJNWmLtmdNVQqkJGFYfM473RTBB1YevKx -p x --gridseed-options=freq=850 --scrypt